In 1979, Marvel gained the license to create comics based on the new movie, Star Trek: The Motion Picture. They were the second publisher to make Trek comics (Gold Key Comics was the first). Marvel began by publishing an oversized adaptation of that movie in the Marvel Super-Size periodical (which was later reissued as the first three installments of a monthly Star Trek series). Their license was limited: the company was given permission only to use copyrighted material based on the movie, and was legally forbidden from reintroducing characters and concepts from The Original Series. This limit was felt by many to be the cause for the short-lived nature of the series. It was canceled after 18 issues, in 1981.

Star Trek had been long-published by other companies by 1997, when Marvel again gained a license to produce new Trek comics, under the imprint of a new line commissioned by Paramount Pictures, entitled Paramount Comics. They began with a controversial crossover, between the original Star Trek crew and the X-Men. They produced several monthly series, including Star Trek: Voyager (the first ever Voyager comic), Star Trek: Deep Space Nine (taking over DS9 from Malibu Comics, a line which Marvel bought and absorbed into their own), Star Trek: Early Voyages (about Captain Pike and crew) and Star Trek: Starfleet Academy (about a group of young cadets including Nog). They also published a quarterly series, Star Trek Unlimited which featured TOS and TNG adventures. Numerous other special issues and crossover books that were not part of these series were also published. Many believe the large influx of Trek comics killed the market: sales dwindled, and most of the series were canceled a year-and-a-half later.